Organic materials for aqueous zinc ion batteries have been attracted the attention of researchers because of their high safety, environmental friendliness, and structural designability. However, the limited specific capacity, unsatisfactory cycling durability, and unclear charge storage mechanism limit their development and applications. Herein, NTCDA-2,3-DNQ, an organic compound with a benzimidazole ring structure, was designed through the number and distribution of active sites as well as the adjustment of molecular weight, and applied as the cathode for aqueous zinc-ion batteries. NTNQ exhibits high specific capacity of 290.5 mAh·g^–1 at 0.05 A·g^–1, excellent rate performance of 133.3 mAh·g^–1 at 15 A·g^–1, and relatively stable cycle life with 81.7% capacity retention over 10,000 superlong cycles at 10 A·g^–1. Furthermore, the synergistic effect of neighboring active sites and multi-electron Zn²⁺ storage reactions are further explored by density functional theory (DFT) calculations, and the results show that NTNQ could stores 4Zn²⁺ while transferring 8e^– in the N-Zn-O pathway during the storage of Zn²⁺. Interestingly, NTNQ still exhibits high specific capacity and favorable cycling stability at multiple ultra-high loadings. This work provides important chances including the design concepts of the organic molecules and the investigation of the Zn²⁺ storage mechanism for high performance aqueous zinc ion batteries.